Re: [gmx-users] Invalid order for directive atomtypes

[Mark Abraham]

On 5/04/2011 4:59 PM, Geethu Issac wrote:

hello friends,

I am doing simulation of ganglioside gm2 and am getting the following 
error.


Fatal error:
Syntax error - File gm2gang.top, line 6
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
Can anyone please help me in this.I am new to gromacs.


Check out http://www.gromacs.org/Documentation/Errors. Also, when asking 
for help, more description would usually be advisable - see 
http://www.gromacs.org/Support.


Cheers,

Mark
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Re: [gmx-users] domain decomposition

[mohsen ramezanpour]

Dear Mark

Actually I don't know why.
I just did the normal process as other my simulations.

Let me discribe my work in details:
I had a protein and a drug,I separated all residues around my drug (2 nm in
radius) by PYMOL
Then I saved the result as protein-new.pdb
So.I used pdb2gmx to generate .top and .gro file for this .pdb file
I entered the following commands for pdb2gmx:
pdb2gmx  -f  protein-new.pdb  -o  protein-new.gro   -p   topology.top
-water  spc  -ignh
and I used Gromos 43a1 force field.

when I want to do EM there are an additional error that  results in crashing
the mdrun:
Warning: 1-4 interaction ...  your system is exploding

it says modifying interaction tables!

Besides,I checked my pdb file,atoms 922 and 943 and 2 others who have bad
interactions,all of them are N atom of residues!

Thanks in advance for your reply






On Sun, Apr 3, 2011 at 8:33 PM, Mark Abraham wrote:

> On 4/04/2011 1:51 AM, mohsen ramezanpour wrote:
>
>> Dear All
>>
>> I have a file which contains afew residues (noncontinuous),
>> When I use mdrun on a computer(4 cpu) I am facing with the following
>> Error:
>>
>> Fatal error:
>> There is no domain decomposition for 4 nodes that is compatible with the
>> given box and a minimum cell size of 3.28697 nm
>> Change the number of nodes or mdrun option -rdd
>> Look in the log file for details on the domain decomposition
>>
>>
>> it is relating to domain decomposition,
>> Besides I checked either restraining residues and not restraining.But it
>> dosn't differed
>>
>> I changed the number of nodes to 1 but it didn't work!
>> mpirun   -np  1  mdrun   -v   -deffnm  EM
>>
>> Besides I looked in the log file and the important part of it was:
>>
>> Initializing Domain Decomposition on 4 nodes
>> Dynamic load balancing: no
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>two-body bonded interactions: 2.988 nm, LJ-14, atoms 922 943
>>  multi-body bonded interactions: 2.988 nm, Proper Dih., atoms 922 943
>> Minimum cell size due to bonded interactions: 3.287 nm
>> Using 0 separate PME nodes
>> Optimizing the DD grid for 4 cells with a minimum initial size of 3.287 nm
>> The maximum allowed number of cells is: X 1 Y 1 Z 1
>>
>>
>> please let me know how can I solve this problem.
>> Thanks in advance
>>
>
> Why do you have bonds nearly 3nm long?
>
> Mark
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Re: [gmx-users] domain decomposition

[Mark Abraham]

On 5/04/2011 5:09 PM, mohsen ramezanpour wrote:

Dear Mark

Actually I don't know why.
I just did the normal process as other my simulations.

Let me discribe my work in details:
I had a protein and a drug,I separated all residues around my drug (2 
nm in radius) by PYMOL


You can't do that and hope for sensible results. The protein won't be 
happy if you expose its hydrophilic core to either a box of solvent or 
vacuum or implicit solvent.



Then I saved the result as protein-new.pdb
So.I used pdb2gmx to generate .top and .gro file for this .pdb file


pdb2gmx assumes you're giving it reasonable input - i.e. no missing 
residues in the protein. However, you've generated several chunks of 
missing residues above. pdb2gmx assumes there's a backbone peptide bond 
as normal, and this is too long. One can work around this issue, but 
still be crippled by the first problem.



I entered the following commands for pdb2gmx:
pdb2gmx  -f  protein-new.pdb  -o  protein-new.gro   -p   topology.top  
-water  spc  -ignh

and I used Gromos 43a1 force field.

when I want to do EM there are an additional error that  results in 
crashing the mdrun:

Warning: 1-4 interaction ...  your system is exploding

it says modifying interaction tables!

Besides,I checked my pdb file,atoms 922 and 943 and 2 others who have 
bad interactions,all of them are N atom of residues!


Yep, pdb2gmx has generated backbone peptide bonds that aren't sensible.

Mark
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Re: [gmx-users] domain decomposition

[mohsen ramezanpour]

Dear Mark

Thank you for your important notes,I didn't know them.

Then,Can it  be resulted from your sentences , there is not any way for
doing simulation with only some parts of  a protein?
What can I do if I need simulating only ACTIVE SITE of a protein?Do I have
to simulate the whole of protein?
Thanks in advance




On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham wrote:

> On 5/04/2011 5:09 PM, mohsen ramezanpour wrote:
>
>> Dear Mark
>>
>> Actually I don't know why.
>> I just did the normal process as other my simulations.
>>
>> Let me discribe my work in details:
>> I had a protein and a drug,I separated all residues around my drug (2 nm
>> in radius) by PYMOL
>>
>
> You can't do that and hope for sensible results. The protein won't be happy
> if you expose its hydrophilic core to either a box of solvent or vacuum or
> implicit solvent.
>
>
>  Then I saved the result as protein-new.pdb
>> So.I used pdb2gmx to generate .top and .gro file for this .pdb file
>>
>
> pdb2gmx assumes you're giving it reasonable input - i.e. no missing
> residues in the protein. However, you've generated several chunks of missing
> residues above. pdb2gmx assumes there's a backbone peptide bond as normal,
> and this is too long. One can work around this issue, but still be crippled
> by the first problem.
>
>
>  I entered the following commands for pdb2gmx:
>> pdb2gmx  -f  protein-new.pdb  -o  protein-new.gro   -p   topology.top
>>  -water  spc  -ignh
>> and I used Gromos 43a1 force field.
>>
>> when I want to do EM there are an additional error that  results in
>> crashing the mdrun:
>> Warning: 1-4 interaction ...  your system is exploding
>>
>> it says modifying interaction tables!
>>
>> Besides,I checked my pdb file,atoms 922 and 943 and 2 others who have bad
>> interactions,all of them are N atom of residues!
>>
>
> Yep, pdb2gmx has generated backbone peptide bonds that aren't sensible.
>
>
> Mark
> --
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Re: [gmx-users] domain decomposition

[Mark Abraham]

On 5/04/2011 5:39 PM, mohsen ramezanpour wrote:

Dear Mark

Thank you for your important notes,I didn't know them.

Then,Can it  be resulted from your sentences , there is not any way 
for doing simulation with only some parts of  a protein?
What can I do if I need simulating only ACTIVE SITE of a protein?Do I 
have to simulate the whole of protein?

Thanks in advance


Generally, yes. For example, it is well known that the electrostatic 
influence of the bulk of the protein affects the function of enzymes. 
Polarization of ligand charge density by the environment can have a 
strong effect on all kinds of chemistry, and is one of the chief 
limitations of trying to use the molecular-mechanics static-point-charge 
model. People spend obscene amounts of resources doing QM+MM MD because 
they need to, not because they have too much computer time! (Even these 
models ignore the polarization of the protein on itself... charges 
parameterized on small-molecule model data need have no relevance near a 
catalytic site...)


Time spent doing background reading can pay off hundred-fold :-)

Mark

On Tue, Apr 5, 2011 at 11:58 AM, Mark Abraham > wrote:


On 5/04/2011 5:09 PM, mohsen ramezanpour wrote:

Dear Mark

Actually I don't know why.
I just did the normal process as other my simulations.

Let me discribe my work in details:
I had a protein and a drug,I separated all residues around my
drug (2 nm in radius) by PYMOL


You can't do that and hope for sensible results. The protein won't
be happy if you expose its hydrophilic core to either a box of
solvent or vacuum or implicit solvent.


Then I saved the result as protein-new.pdb
So.I used pdb2gmx to generate .top and .gro file for this .pdb
file


pdb2gmx assumes you're giving it reasonable input - i.e. no
missing residues in the protein. However, you've generated several
chunks of missing residues above. pdb2gmx assumes there's a
backbone peptide bond as normal, and this is too long. One can
work around this issue, but still be crippled by the first problem.


I entered the following commands for pdb2gmx:
pdb2gmx  -f  protein-new.pdb  -o  protein-new.gro   -p  
topology.top  -water  spc  -ignh

and I used Gromos 43a1 force field.

when I want to do EM there are an additional error that
 results in crashing the mdrun:
Warning: 1-4 interaction ...  your system is exploding

it says modifying interaction tables!

Besides,I checked my pdb file,atoms 922 and 943 and 2 others
who have bad interactions,all of them are N atom of residues!


Yep, pdb2gmx has generated backbone peptide bonds that aren't
sensible.


Mark
-- 
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Re: [gmx-users] the total charge of system is not an integer

[ahmet yıldırım]

Dear Mark,

Now, are the files correct?
*EDO.itp*:
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO OAB 1   -0.111  15.9994
 2 H   1  EDO HAE 10.031   1.0080
 3   CH2 1  EDO CAA 10.080  14.0270
 4   CH2 1  EDO CAC *2*0.080  14.0270
 5OA 1  EDO OAD *2*   -0.111  15.9994
 6 H   1  EDO HAF *2 *   0.031   1.0080

*TRS.itp:*
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.119  15.9994
 2 H 1  TRS  H13 10.032   1.0080
 3   CH2 1  TRS  C1 10.087  14.0270
 4  CCl4 1  TRSC *3*0.055  12.0110
 5   CH2 1  TRS  C3* 4 *   0.049  14.0270
 6OA 1  TRS  O3 *4*   -0.205  15.9994
 7 H 1  TRS  H33* 4*0.019   1.0080
 8NL 1  TRS N* 5*0.206  14.0067
 9 H 1  TRS H2   * 5*0.004   1.0080
10 H 1  TRSH3 *5*0.004   1.0080
11 H 1  TRSH1 *5 *  0.004   1.0080
12   CH2 1  TRS  C2 *6 *   0.150  14.0270
13OA 1  TRS  O2 *6*   -0.205  15.9994
14 H 1  TRS  H23* 6*0.019   1.0080

Thanks for your helps

05 Nisan 2011 09:03 tarihinde Mark Abraham  yazdı:

>  On 5/04/2011 3:57 PM, ahmet yıldırım wrote:
>
> Dear Tsjerk,
>
> Hi Ahmet,
>>
>> As suggested, it's better to break up your molecule into smaller
>> charge groups. Note that charge groups don't need to have zero charge,
>> nor integer charge. In your case, I'd suggest two COH groups for EDO,
>> which will have zero net charge each, and for TRS I'd take the COH
>> groups as separate charge groups. I also note that the COH groups,
>> although chemically identical - H3NC(COH)3, right?-, have different
>> charges. That doesn't seem proper.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>
> nonrevised .itp file:
> EDO  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1OA 1  EDO OAB 1   -0.111  15.9994
>  2 H 1  EDO HAE 10.031   1.0080
>  3   CH2 1  EDO CAA 10.080  14.0270
>  4   CH2 1  EDO CAC 10.080  14.0270
>  5OA 1  EDO OAD 1   -0.111  15.9994
>  6 H 1  EDO HAF 10.031   1.0080
>
> nonrevised .itp file:
> EDO  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1OA 1  EDO OAB 1   -0.111  15.9994
>  2 H 1  EDO HAE 10.031   1.0080
>  3   CH2 1  EDO CAA 1*0.000*  14.0270
>  4   CH2 1  EDO CAC 1*0.000*  14.0270
>  5OA 1  EDO OAD 1   -0.111  15.9994
>  6 H 1  EDO HAF 10.031   1.0080
>
> can you show me on the itp file? how do I seperate two COH groups? Please
> help me
>
>
> We didn't say to use zero *charges*. We said you need small charge groups.
> Since EDO is neutral, then by symmetry each half must also be neutral.
>
> Have a look at the way charge groups are used in the .rtp file for your
> forcefield. You need to do similar things. If you don't understand the file
> formats yet, you need to read up on chapter 5 of the manual.
>
> Mark
>
> --
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-- 
Ahmet YILDIRIM
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[gmx-users] OPLS-AA atom types

[Austin B. Yongye]

Hello GROMACS USERS,
Does any one have a document/manual/link that describes the name-number atom 
type mappings employed in opls-aa?

I would like to build some molecules and specify their parameters, but I see 
different of numbers for the same atom type name, e.g:

TYPE NAME
135  CT
136  CT
137  CT
157  CT

I can deduce that 135 is CH3-, 136 is R-CH2-, and 137 is RRCH- by looking at 
topology files.
Thanks,
Austin-
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Re: [gmx-users] OPLS-AA atom types

[Justin A. Lemkul]

Austin B. Yongye wrote:

Hello GROMACS USERS,
Does any one have a document/manual/link that describes the name-number atom 
type mappings employed in opls-aa?



The correspondence between the atom types and bonded types is all contained in 
ffnonbonded.itp.


-Justin


I would like to build some molecules and specify their parameters, but I see 
different of numbers for the same atom type name, e.g:

TYPE NAME
135  CT
136  CT
137  CT
157  CT

I can deduce that 135 is CH3-, 136 is R-CH2-, and 137 is RRCH- by looking at 
topology files.
Thanks,
Austin-


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] OPLS-AA atom types

[Austin B. Yongye]

Thanks Justin.
Could you/someone please forward the file? I don't have it.
Austin-

--- On Tue, 4/5/11, Justin A. Lemkul  wrote:

> From: Justin A. Lemkul 
> Subject: Re: [gmx-users] OPLS-AA atom types
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, April 5, 2011, 5:19 AM
> 
> 
> Austin B. Yongye wrote:
> > Hello GROMACS USERS,
> > Does any one have a document/manual/link that
> describes the name-number atom type mappings employed in
> opls-aa?
> > 
> 
> The correspondence between the atom types and bonded types
> is all contained in ffnonbonded.itp.
> 
> -Justin
> 
> > I would like to build some molecules and specify their
> parameters, but I see different of numbers for the same atom
> type name, e.g:
> > 
> > TYPE NAME
> > 135  CT
> > 136  CT
> > 137  CT
> > 157  CT
> > 
> > I can deduce that 135 is CH3-, 136 is R-CH2-, and 137
> is RRCH- by looking at topology files.
> > Thanks,
> > Austin-
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- gmx-users mailing list    gmx-users@gromacs.org
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Re: [gmx-users] OPLS-AA atom types

[Justin A. Lemkul]

Austin B. Yongye wrote:

Thanks Justin.
Could you/someone please forward the file? I don't have it.


It's part of your Gromacs installation.  $GMXLIB/oplsaa.ff/ffnonbonded.itp.

If you don't have it, then Gromacs wasn't properly installed and you won't be 
able to use whatever force field for which you're designing your topologies.


-Justin


Austin-

--- On Tue, 4/5/11, Justin A. Lemkul  wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users" 
Date: Tuesday, April 5, 2011, 5:19 AM


Austin B. Yongye wrote:

Hello GROMACS USERS,
Does any one have a document/manual/link that

describes the name-number atom type mappings employed in
opls-aa?
The correspondence between the atom types and bonded types
is all contained in ffnonbonded.itp.

-Justin


I would like to build some molecules and specify their

parameters, but I see different of numbers for the same atom
type name, e.g:

TYPE NAME
135  CT
136  CT
137  CT
157  CT

I can deduce that 135 is CH3-, 136 is R-CH2-, and 137

is RRCH- by looking at topology files.

Thanks,
Austin-

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] the total charge of system is not an integer

[Mark Abraham]

On 5/04/2011 9:59 PM, ahmet yıldırım wrote:

Dear Mark,

Now, are the files correct?


They're well-formed, but you've not taken Tsjerk's advice and arranged 
for (COH)3(NH3+)C to have charges consistent with its symmetry. When 
people donate their time to you, please use it or demonstrate why you 
shouldn't :-)


Mark


*EDO.itp*:
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO OAB 1   -0.111  15.9994
 2 H   1  EDO HAE 10.031   1.0080
 3   CH2 1  EDO CAA 10.080  14.0270
 4   CH2 1  EDO CAC *2*0.080  14.0270
 5OA 1  EDO OAD *2*   -0.111  15.9994
 6 H   1  EDO HAF *2 *   0.031   1.0080

*TRS.itp:*
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.119  15.9994
 2 H 1  TRS  H13 10.032   1.0080
 3   CH2 1  TRS  C1 10.087  14.0270
 4  CCl4 1  TRSC *3*0.055  12.0110
 5   CH2 1  TRS  C3 *4 *   0.049  14.0270
 6OA 1  TRS  O3 *4*   -0.205  15.9994
 7 H 1  TRS  H33 *4*0.019   1.0080
 8NL 1  TRS N *5*0.206  14.0067
 9 H 1  TRS H2 *5*0.004   1.0080
10 H 1  TRSH3 *5*0.004   1.0080
11 H 1  TRSH1 *5 *  0.004   1.0080
12   CH2 1  TRS  C2 *6 *   0.150  14.0270
13OA 1  TRS  O2 *6*   -0.205  15.9994
14 H 1  TRS  H23 *6*0.019   1.0080

Thanks for your helps

05 Nisan 2011 09:03 tarihinde Mark Abraham > yazdı:


On 5/04/2011 3:57 PM, ahmet yıldırım wrote:

Dear Tsjerk,

Hi Ahmet,

As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have
zero charge,
nor integer charge. In your case, I'd suggest two COH groups
for EDO,
which will have zero net charge each, and for TRS I'd take
the COH
groups as separate charge groups. I also note that the COH
groups,
although chemically identical - H3NC(COH)3, right?-, have
different
charges. That doesn't seem proper.

Hope it helps,

Tsjerk


nonrevised .itp file:
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO OAB 1   -0.111  15.9994
 2 H 1  EDO HAE 10.031   1.0080
 3   CH2 1  EDO CAA 10.080  14.0270
 4   CH2 1  EDO CAC 10.080  14.0270
 5OA 1  EDO OAD 1   -0.111  15.9994
 6 H 1  EDO HAF 10.031   1.0080

nonrevised .itp file:
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO OAB 1   -0.111  15.9994
 2 H 1  EDO HAE 10.031   1.0080
 3   CH2 1  EDO CAA 1 *0.000*  14.0270
 4   CH2 1  EDO CAC 1 *0.000*  14.0270
 5OA 1  EDO OAD 1   -0.111  15.9994
 6 H 1  EDO HAF 10.031   1.0080

can you show me on the itp file? how do I seperate two COH
groups? Please help me


We didn't say to use zero *charges*. We said you need small charge
groups. Since EDO is neutral, then by symmetry each half must also
be neutral.

Have a look at the way charge groups are used in the .rtp file for
your forcefield. You need to do similar things. If you don't
understand the file formats yet, you need to read up on chapter 5
of the manual.

Mark

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Re: [gmx-users] OPLS-AA atom types

[Mark Abraham]

On 5/04/2011 11:03 PM, Austin B. Yongye wrote:

Thanks Justin.
Could you/someone please forward the file? I don't have it.
Austin-


Announcing your GROMACS version is an excellent idea. See 
http://www.gromacs.org/Support for good suggestions when asking for free 
help.


Because you haven't, we have to suppose that either your installation is 
broken, you're not looking at it properly, or you're using a version 
before 4.0 that has the information in a file with a different name.


Mark



--- On Tue, 4/5/11, Justin A. Lemkul  wrote:


From: Justin A. Lemkul
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users"
Date: Tuesday, April 5, 2011, 5:19 AM


Austin B. Yongye wrote:

Hello GROMACS USERS,
Does any one have a document/manual/link that

describes the name-number atom type mappings employed in
opls-aa?
The correspondence between the atom types and bonded types
is all contained in ffnonbonded.itp.

-Justin


I would like to build some molecules and specify their

parameters, but I see different of numbers for the same atom
type name, e.g:

TYPE NAME
135  CT
136  CT
137  CT
157  CT

I can deduce that 135 is CH3-, 136 is R-CH2-, and 137

is RRCH- by looking at topology files.

Thanks,
Austin-

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] How to remove charge of 5e-2 ??

[Hyunsik]

Dear experts,

Hi, 

When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.

But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove 
that.

i want to make totally neutral system.

Thank you.

Hyun--
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Re: [gmx-users] How to remove charge of 5e-2 ??

[Justin A. Lemkul]

Hyunsik wrote:

Dear experts,

Hi, 


When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.

But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove 
that.

i want to make totally neutral system.



Fractional charges like these indicate that your topology is broken.  Check its 
contents (especially the qtot running total if the .top was created by pdb2gmx).


-Justin


Thank you.

Hyun-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] How to remove charge of 5e-2 ??

[Mark Abraham]

On 5/04/2011 11:17 PM, Hyunsik wrote:

Dear experts,

Hi,

When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.

But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove 
that.


Your statements are inconsistent. If you had 5.5 charge and added five 
chloride ions, you could not end up with 0.05.


Mark
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[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

[Pablo Englebienne]

Hi all,

I'm trying to compile release 4.5.4 on a system that has been running 
every release since 4.0.4 without a problem. Even 4.5.3 compiled fine 
with the following configure:


LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib" 
CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure 
--prefix=$HOME/software


The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW 
libraries and headers. Configure succeeds in creating the Makefiles, but 
when running make it aborts at this point:


cc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o .libs/coupling.o 
.libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o .libs/domdec_network.o 
.libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o 
.libs/ewald.o .libs/force.o .libs/forcerec.o .libs/ghat.o .libs/init.o 
.libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o 
.libs/nsgrid.o .libs/perf_est.o .libs/genborn.o .libs/genborn_sse2_single.o 
.libs/genborn_sse2_double.o .libs/genborn_allvsall.o 
.libs/genborn_allvsall_sse2_single.o .libs/genborn_allvsall_sse2_double.o 
.libs/gmx_qhop_parm.o .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o 
.libs/pme_pp.o .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o 
.libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o .libs/stat.o 
.libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o .libs/vcm.o 
.libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o .libs/clincs.o 
.libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o .libs/fft5d.o 
.libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o .libs/qm_gamess.o 
.libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o .libs/gmx_fft_fftpack.o 
.libs/gmx_fft_mkl.o .libs/qm_orca.o .libs/mdebin_bar.o  -Wl,--rpath 
-Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath 
-Wl,/home/penglebie/software/lib 
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2 
-L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl -lm  
-msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0
/usr/bin/ld: 
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o): 
relocation R_X86_64_32 against `a local symbol' can not be used when making a 
shared object; recompile with -fPIC
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a: could not read symbols: Bad 
value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
make: *** [all-recursive] Error 1

I see that recently 
(http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html) 
another user encountered the same problem but this time with version 
4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4.


The system is running Scientific Linux 5.5.

$ uname -a

Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 
x86_64 x86_64 GNU/Linux


I am puzzled as to why it doesn't work in 4.5.4 but did until the 
previous release. Did something change in this respect?


Regards,
Pablo

--
Pablo Englebienne, PhD
Dept. of Biomedical Engineering
Dept. of Chemistry and Chemical Engineering
Institute for Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349


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Re: [gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

[Justin A. Lemkul]

Pablo Englebienne wrote:

Hi all,

I'm trying to compile release 4.5.4 on a system that has been running 
every release since 4.0.4 without a problem. Even 4.5.3 compiled fine 
with the following configure:


LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib" 
CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure 
--prefix=$HOME/software


The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW 
libraries and headers. Configure succeeds in creating the Makefiles, but 
when running make it aborts at this point:


cc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o 
.libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o 
.libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o 
.libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o 
.libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o 
.libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o 
.libs/genborn_sse2_single.o .libs/genborn_sse2_double.o 
.libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o 
.libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o 
.libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o 
.libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o 
.libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o 
.libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o 
.libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o 
.libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o 
.libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o 
.libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o 
.libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o 
.libs/mdebin_bar.o  -Wl,--rpath 
-Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath 
-Wl,/home/penglebie/software/lib 
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2 
-L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl 
-lm  -msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0
/usr/bin/ld: 
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o): 
relocation R_X86_64_32 against `a local symbol' can not be used when 
making a shared object; recompile with -fPIC
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a: could not read 
symbols: Bad value

collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory 
`/home/penglebie/downloads/gromacs-4.5.4/src/mdlib'

make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
make: *** [all-recursive] Error 1

I see that recently 
(http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html) 
another user encountered the same problem but this time with version 
4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4.




The solution is discussed in the installation instructions:

http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites


The system is running Scientific Linux 5.5.

$ uname -a

Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 
x86_64 x86_64 x86_64 GNU/Linux



I am puzzled as to why it doesn't work in 4.5.4 but did until the 
previous release. Did something change in this respect?




Maybe, but the fact that this issue has come up numerous times in several 
versions suggests not.  As for why 4.5.3 works and 4.5.4 doesn't, I can't say 
specifically.  Please follow the instructions linked above and see if it fixes 
your problem.


-Justin


Regards,
Pablo



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] OPLS-AA atom types

[Austin B. Yongye]

Justin:
I am using gromacs version 4.0.2. Several attempts to download current gromacs 
versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files. 
So I re-installed my pre-existing v4.0.2 without any problems (>./configure 
--enable-sse; make; make install).
If you could send me the ffnonbonded.itp file that would be great.
Austin-

--- On Tue, 4/5/11, Justin A. Lemkul  wrote:

> From: Justin A. Lemkul 
> Subject: Re: [gmx-users] OPLS-AA atom types
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, April 5, 2011, 6:06 AM
> 
> 
> Austin B. Yongye wrote:
> > Thanks Justin.
> > Could you/someone please forward the file? I don't
> have it.
> 
> It's part of your Gromacs installation. 
> $GMXLIB/oplsaa.ff/ffnonbonded.itp.
> 
> If you don't have it, then Gromacs wasn't properly
> installed and you won't be 
> able to use whatever force field for which you're designing
> your topologies.
> 
> -Justin
> 
> > Austin-
> > 
> > --- On Tue, 4/5/11, Justin A. Lemkul 
> wrote:
> > 
> >> From: Justin A. Lemkul 
> >> Subject: Re: [gmx-users] OPLS-AA atom types
> >> To: "Discussion list for GROMACS users" 
> >> Date: Tuesday, April 5, 2011, 5:19 AM
> >>
> >>
> >> Austin B. Yongye wrote:
> >>> Hello GROMACS USERS,
> >>> Does any one have a document/manual/link that
> >> describes the name-number atom type mappings
> employed in
> >> opls-aa?
> >> The correspondence between the atom types and
> bonded types
> >> is all contained in ffnonbonded.itp.
> >>
> >> -Justin
> >>
> >>> I would like to build some molecules and
> specify their
> >> parameters, but I see different of numbers for the
> same atom
> >> type name, e.g:
> >>> TYPE NAME
> >>> 135  CT
> >>> 136  CT
> >>> 137  CT
> >>> 157  CT
> >>>
> >>> I can deduce that 135 is CH3-, 136 is R-CH2-,
> and 137
> >> is RRCH- by looking at topology files.
> >>> Thanks,
> >>> Austin-
> >> -- 
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> 
> >> -- gmx-users mailing list    gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at 
> >> http://www.gromacs.org/Support/Mailing_Lists/Search
> >> before posting!
> >> Please don't post (un)subscribe requests to the
> list. Use
> >> the www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
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> http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
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> the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] OPLS-AA atom types

[Justin A. Lemkul]

Austin B. Yongye wrote:

Justin:
I am using gromacs version 4.0.2. Several attempts to download current gromacs 
versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files. So I 
re-installed my pre-existing v4.0.2 without any problems (>./configure 
--enable-sse; make; make install).
If you could send me the ffnonbonded.itp file that would be great.


You don't need it.  The corresponding file in 4.0.2 is called ffoplsaanb.itp. 
Newer Gromacs versions have a different directory and naming structure, but the 
contents of these files is the same.


Be aware that there have been dozens (if not hundreds) of usability upgrades, 
bug fixes, and new features that have been added since 4.0.2.  You would be 
well-served to try to figure out why you can't download a newer version.


-Justin


Austin-

--- On Tue, 4/5/11, Justin A. Lemkul  wrote:


From: Justin A. Lemkul 
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users" 
Date: Tuesday, April 5, 2011, 6:06 AM


Austin B. Yongye wrote:

Thanks Justin.
Could you/someone please forward the file? I don't

have it.

It's part of your Gromacs installation. 
$GMXLIB/oplsaa.ff/ffnonbonded.itp.


If you don't have it, then Gromacs wasn't properly
installed and you won't be 
able to use whatever force field for which you're designing

your topologies.

-Justin


Austin-

--- On Tue, 4/5/11, Justin A. Lemkul 

wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users" 
Date: Tuesday, April 5, 2011, 5:19 AM


Austin B. Yongye wrote:

Hello GROMACS USERS,
Does any one have a document/manual/link that

describes the name-number atom type mappings

employed in

opls-aa?
The correspondence between the atom types and

bonded types

is all contained in ffnonbonded.itp.

-Justin


I would like to build some molecules and

specify their

parameters, but I see different of numbers for the

same atom

type name, e.g:

TYPE NAME
135  CT
136  CT
137  CT
157  CT

I can deduce that 135 is CH3-, 136 is R-CH2-,

and 137

is RRCH- by looking at topology files.

Thanks,
Austin-

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- gmx-users mailing listgmx-users@gromacs.org
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] OPLS-AA atom types

[Austin B. Yongye]

Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances of CT with 
diferent opls_??? numbers, but no indication of their environments; they could 
represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I 
contacted one of the opls folks last week, but got no response. So I thought I 
could enlist the help of gromacs users.
But thanks for your responses anyway.
Austin-

--- On Tue, 4/5/11, Justin A. Lemkul  wrote:

> From: Justin A. Lemkul 
> Subject: Re: [gmx-users] OPLS-AA atom types
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, April 5, 2011, 7:32 AM
> 
> 
> Austin B. Yongye wrote:
> > Justin:
> > I am using gromacs version 4.0.2. Several attempts to
> download current gromacs versions from http://www.gromacs.org/Downloads kept 
> yielding
> 93.0-byte files. So I re-installed my pre-existing v4.0.2
> without any problems (>./configure --enable-sse; make;
> make install).
> > If you could send me the ffnonbonded.itp file that
> would be great.
> 
> You don't need it.  The corresponding file in 4.0.2 is
> called ffoplsaanb.itp. Newer Gromacs versions have a
> different directory and naming structure, but the contents
> of these files is the same.
> 
> Be aware that there have been dozens (if not hundreds) of
> usability upgrades, bug fixes, and new features that have
> been added since 4.0.2.  You would be well-served to
> try to figure out why you can't download a newer version.
> 
> -Justin
> 
> > Austin-
> > 
> > --- On Tue, 4/5/11, Justin A. Lemkul 
> wrote:
> > 
> >> From: Justin A. Lemkul 
> >> Subject: Re: [gmx-users] OPLS-AA atom types
> >> To: "Discussion list for GROMACS users" 
> >> Date: Tuesday, April 5, 2011, 6:06 AM
> >> 
> >> 
> >> Austin B. Yongye wrote:
> >>> Thanks Justin.
> >>> Could you/someone please forward the file? I
> don't
> >> have it.
> >> 
> >> It's part of your Gromacs installation.
> $GMXLIB/oplsaa.ff/ffnonbonded.itp.
> >> 
> >> If you don't have it, then Gromacs wasn't
> properly
> >> installed and you won't be able to use whatever
> force field for which you're designing
> >> your topologies.
> >> 
> >> -Justin
> >> 
> >>> Austin-
> >>> 
> >>> --- On Tue, 4/5/11, Justin A. Lemkul 
> >> wrote:
>  From: Justin A. Lemkul 
>  Subject: Re: [gmx-users] OPLS-AA atom
> types
>  To: "Discussion list for GROMACS users"
> 
>  Date: Tuesday, April 5, 2011, 5:19 AM
>  
>  
>  Austin B. Yongye wrote:
> > Hello GROMACS USERS,
> > Does any one have a
> document/manual/link that
>  describes the name-number atom type
> mappings
> >> employed in
>  opls-aa?
>  The correspondence between the atom types
> and
> >> bonded types
>  is all contained in ffnonbonded.itp.
>  
>  -Justin
>  
> > I would like to build some molecules
> and
> >> specify their
>  parameters, but I see different of numbers
> for the
> >> same atom
>  type name, e.g:
> > TYPE NAME
> > 135  CT
> > 136  CT
> > 137  CT
> > 157  CT
> > 
> > I can deduce that 135 is CH3-, 136 is
> R-CH2-,
> >> and 137
>  is RRCH- by looking at topology files.
> > Thanks,
> > Austin-
>  --
> 
>  
>  Justin A. Lemkul
>  Ph.D. Candidate
>  ICTAS Doctoral Scholar
>  MILES-IGERT Trainee
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  
>  
>  -- gmx-users mailing list    gmx-users@gromacs.org
>  http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at 
>  http://www.gromacs.org/Support/Mailing_Lists/Search
>  before posting!
>  Please don't post (un)subscribe requests
> to the
> >> list. Use
>  the www interface or send it to gmx-users-requ...@gromacs.org.
>  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  
> >> -- 
> >> 
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> 
> >> 
> >> -- gmx-users mailing list    gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at 
> >> http://www.gromacs.org/Support/Mailing_Lists/Search
> >> before posting!
> >> Please don't post (un)subscribe requests to the
> list. Use
> >> the www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> 
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of B

Re: [gmx-users] OPLS-AA atom types

[Mark Abraham]

On 6/04/2011 1:00 AM, Austin B. Yongye wrote:

Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances of CT with 
diferent opls_??? numbers, but no indication of their environments; they could 
represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I 
contacted one of the opls folks last week, but got no response. So I thought I 
could enlist the help of gromacs users.


Yes, but you're making it hard to help you by forcing us to guess what 
content you're looking at. Our time is valuable, and you're not making 
it easy for us to give the minimum amount :-) Tell us what file you 
looked at, what you saw (copy and paste), and why it's not useful.


Mark


But thanks for your responses anyway.
Austin-

--- On Tue, 4/5/11, Justin A. Lemkul  wrote:


From: Justin A. Lemkul
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users"
Date: Tuesday, April 5, 2011, 7:32 AM


Austin B. Yongye wrote:

Justin:
I am using gromacs version 4.0.2. Several attempts to

download current gromacs versions from http://www.gromacs.org/Downloads kept 
yielding
93.0-byte files. So I re-installed my pre-existing v4.0.2
without any problems (>./configure --enable-sse; make;
make install).

If you could send me the ffnonbonded.itp file that

would be great.

You don't need it.  The corresponding file in 4.0.2 is
called ffoplsaanb.itp. Newer Gromacs versions have a
different directory and naming structure, but the contents
of these files is the same.

Be aware that there have been dozens (if not hundreds) of
usability upgrades, bug fixes, and new features that have
been added since 4.0.2.  You would be well-served to
try to figure out why you can't download a newer version.

-Justin


Austin-

--- On Tue, 4/5/11, Justin A. Lemkul

wrote:

From: Justin A. Lemkul
Subject: Re: [gmx-users] OPLS-AA atom types
To: "Discussion list for GROMACS users"
Date: Tuesday, April 5, 2011, 6:06 AM


Austin B. Yongye wrote:

Thanks Justin.
Could you/someone please forward the file? I

don't

have it.

It's part of your Gromacs installation.

$GMXLIB/oplsaa.ff/ffnonbonded.itp.

If you don't have it, then Gromacs wasn't

properly

installed and you won't be able to use whatever

force field for which you're designing

your topologies.

-Justin


Austin-

--- On Tue, 4/5/11, Justin A. Lemkul

wrote:

From: Justin A. Lemkul
Subject: Re: [gmx-users] OPLS-AA atom

types

To: "Discussion list for GROMACS users"



Date: Tuesday, April 5, 2011, 5:19 AM


Austin B. Yongye wrote:

Hello GROMACS USERS,
Does any one have a

document/manual/link that

describes the name-number atom type

mappings

employed in

opls-aa?
The correspondence between the atom types

and

bonded types

is all contained in ffnonbonded.itp.

-Justin


I would like to build some molecules

and

specify their

parameters, but I see different of numbers

for the

same atom

type name, e.g:

TYPE NAME
135  CT
136  CT
137  CT
157  CT

I can deduce that 135 is CH3-, 136 is

R-CH2-,

and 137

is RRCH- by looking at topology files.

Thanks,
Austin-

--



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
Please don't post (un)subscribe requests

to the

list. Use

the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
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list. Use

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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!

Re: [gmx-users] OPLS-AA atom types

[Mark Abraham]

On 6/04/2011 1:28 AM, Mark Abraham wrote:

On 6/04/2011 1:00 AM, Austin B. Yongye wrote:

Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances 
of CT with diferent opls_??? numbers, but no indication of their 
environments; they could represent C bonded to 1->4 carbon atoms, 
etc. There's no way of telling. I contacted one of the opls folks 
last week, but got no response. So I thought I could enlist the help 
of gromacs users.


Yes, but you're making it hard to help you by forcing us to guess what 
content you're looking at. Our time is valuable, and you're not making 
it easy for us to give the minimum amount :-) Tell us what file you 
looked at, what you saw (copy and paste), and why it's not useful.


Ah, I see the problem. Justin recommended the wrong file, and you didn't 
guess the right one from the filenames. You should look at 
atomtypes.atp, and literature references therein.


Mark
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Re: [gmx-users] OPLS-AA atom types

[Justin A. Lemkul]

Mark Abraham wrote:

On 6/04/2011 1:28 AM, Mark Abraham wrote:

On 6/04/2011 1:00 AM, Austin B. Yongye wrote:

Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances 
of CT with diferent opls_??? numbers, but no indication of their 
environments; they could represent C bonded to 1->4 carbon atoms, 
etc. There's no way of telling. I contacted one of the opls folks 
last week, but got no response. So I thought I could enlist the help 
of gromacs users.


Yes, but you're making it hard to help you by forcing us to guess what 
content you're looking at. Our time is valuable, and you're not making 
it easy for us to give the minimum amount :-) Tell us what file you 
looked at, what you saw (copy and paste), and why it's not useful.


Ah, I see the problem. Justin recommended the wrong file, and you didn't 
guess the right one from the filenames. You should look at 
atomtypes.atp, and literature references therein.


Based on the original question (mapping between names and numbers), I thought I 
had provided the requested information.  If I've ended up wasting anyone's time, 
I apologize.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] ffbonded.itp file

[anna . marabotti]

Dear gmx-users,
I’m trying to modify the ffbonded.itp file of Gromos43a1 ff in Gromacs
4.5.3 version, in order to add parameters for my modified Cys residue.
However, I have some difficulties in understanding what are the
parameters already included in this file. In particular, ffbonded.itp
file appears as:

; Table 2.5.2.1
;   GROMOS bond-stretching parameters
;
;
;   Bond type code
;   Force constant
;   Ideal bond length
;   Examples of usage in terms of non-bonded atom types
;
;
;   ICB(H)[N]CB[N] B0[N]
;
#define gb_10.1000  1.5700e+07
; H  -  OA  750
;
#define gb_20.1000  1.8700e+07
; H  -  N (all) 895
;
#define gb_30.1090  1.2300e+07
; HC  -  C  700


but while I understand the meaning of the first two numbers, I don’t
understand what the number near the description of the two atom type is
(for example, in the definition of gb_3, what is “700” after HC – C? I
looked at the Manual of Gromacs version 4.5.3, section 5, paragraph
5.3.3. Bonds (page 111) but the “example excerpt” for ffbonded.itp file
is very different from the one I see in my ffG43a1 directory! I don’t
see in the manual or elsewhere a detailed explanation for the meaning of
each component of this file. Could you please help me?
Moreover, I see some strange definitions, at least in my opinion. I’m
trying to mutuate parameters from DMSO: (CH3)2S=O. Under the section
Bond type, I see these definitions:

#define gb_44 0.280412  2.3900e+06
; ODmso -   CDmso900
;
#define gb_45 0.292993  2.1900e+06
; CDmso -   CDmso900

I really don’t understand the sense of the definition of these bonds
types, provided that they are absent in DMSO since the two methyl groups
are linked only to sulphur, not to each others (no C-C bond) and that
oxygen is linked only to sulphur (no O-C bond). Could you please check
for these strange interactions, or am I mistakenly interpreting them?
Thank you very much and best regards
Anna Marabotti
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Re: [gmx-users] ffbonded.itp file

[Justin A. Lemkul]

anna.marabo...@isa.cnr.it wrote:

Dear gmx-users,
I’m trying to modify the ffbonded.itp file of Gromos43a1 ff in Gromacs
4.5.3 version, in order to add parameters for my modified Cys residue.
However, I have some difficulties in understanding what are the
parameters already included in this file. In particular, ffbonded.itp
file appears as:

; Table 2.5.2.1
;   GROMOS bond-stretching parameters
;
;
;   Bond type code
;   Force constant
;   Ideal bond length
;   Examples of usage in terms of non-bonded atom types
;
;
;   ICB(H)[N]CB[N] B0[N]
;
#define gb_10.1000  1.5700e+07
; H  -  OA  750
;
#define gb_20.1000  1.8700e+07
; H  -  N (all) 895
;
#define gb_30.1090  1.2300e+07
; HC  -  C  700


but while I understand the meaning of the first two numbers, I don’t
understand what the number near the description of the two atom type is
(for example, in the definition of gb_3, what is “700” after HC – C? I


These are index values, which I believe were ported from the Gromos software 
eons ago.  They have no meaning in the context of Gromacs (and you'll note that 
it's a comment, anyway).  The necessary parameters are all contained within the 
#define statements, which are then mapped back to the topology when invoked.



looked at the Manual of Gromacs version 4.5.3, section 5, paragraph
5.3.3. Bonds (page 111) but the “example excerpt” for ffbonded.itp file
is very different from the one I see in my ffG43a1 directory! I don’t


The Gromos force fields are somewhat unique.  The parameters are assigned based 
on #define statements.  All the other force fields follow the format shown in 
the manual, so the documentation reflects the most general case (which, as 
implied by the #defines, is still effectively maintained here).



see in the manual or elsewhere a detailed explanation for the meaning of
each component of this file. Could you please help me?
Moreover, I see some strange definitions, at least in my opinion. I’m
trying to mutuate parameters from DMSO: (CH3)2S=O. Under the section
Bond type, I see these definitions:

#define gb_44 0.280412  2.3900e+06
; ODmso -   CDmso900
;
#define gb_45 0.292993  2.1900e+06
; CDmso -   CDmso900

I really don’t understand the sense of the definition of these bonds
types, provided that they are absent in DMSO since the two methyl groups
are linked only to sulphur, not to each others (no C-C bond) and that
oxygen is linked only to sulphur (no O-C bond). Could you please check
for these strange interactions, or am I mistakenly interpreting them?


These are not bonds in the sense of true chemical covalent bonds, but rather 
they are used to fix the geometry of DMSO.  I am not aware of any publications 
on the 43A1 DMSO parameters (although 53A6 DMSO does have a publication, and 
since the same bonds are present you might investigate that particular paper...I 
think it was in J Phys Chem B), which makes it hard to confirm the purpose of 
these "bonds."  Presumably, since all Gromos solvent models are rigid, these are 
present to force some geometry, as is the case with, e.g. CHCl3.


-Justin


Thank you very much and best regards
Anna Marabotti


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] invalid line

[sarah k]

dear gromacs users,

I'm solvating my protein in nitrogen box. I have changed my
spc216.gro, spc.itp and spce.itp files. I face the following error.
How can I fix it?

invalid line in /usr/share/gromacs/top/spc216.gro for atom 407:
  0.41200  0.41200  0.41200

thanks in advance.

Best regards,
Fatemeh Keshavarz
 203N2,DRGJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
  430
1SOL N11.230.628.113
1SOL N22.137.626.150
2SOL N13.225.275   -.866
2SOL N24.260.258   -.774
3SOL N15.019.368.647
3SOL N26   -.063.411.686
4SOL N17.569   -.587   -.697
4SOL N28.476   -.594   -.734
5SOL N19   -.307   -.351.703
5SOL N2   10   -.364   -.367.784
6SOL N1   11   -.119.618.856
6SOL N2   12   -.086.712.856
7SOL N1   13   -.727.703.717
7SOL N2   14   -.670.781.692
8SOL N1   15   -.107.607.231
8SOL N2   16   -.119.594.132
9SOL N1   17.768   -.718   -.839
9SOL N2   18.690   -.701   -.779
   10SOL N1   19.850.798   -.039
   10SOL N2   20.846.874.026
   11SOL N1   21.685   -.850.665
   11SOL N2   22.754   -.866.735
   12SOL N1   23.686   -.701   -.059
   12SOL N2   24.746   -.622   -.045
   13SOL N1   25.335   -.427   -.801
   13SOL N2   27.257   -.458   -.854
   14SOL N1   28   -.402   -.357   -.523
   14SOL N2   29   -.378   -.263   -.497
   15SOL N1   30.438.392   -.363
   15SOL N2   31.520.336   -.354
   16SOL N1   32   -.259.447.737
   16SOL N2   33   -.333.493.687
   17SOL N1   34.231   -.149.483
   17SOL N2   35.265   -.072.537
   18SOL N1   36   -.735   -.521   -.172
   18SOL N2   37   -.688   -.521   -.084
   19SOL N1   38.230   -.428.538
   19SOL N2   39.204   -.332.538
   20SOL N1   40.240   -.771.886
   20SOL N2   41.254   -.855.938
   21SOL N1   42.620   -.076   -.423
   21SOL N2   43.528   -.093   -.388
   22SOL N1   44.606   -.898.123
   22SOL N2   45.613   -.814.069
   23SOL N1   46   -.268.114   -.382
   23SOL N2   47   -.286.181   -.454
   24SOL N1   48.122.643.563
   24SOL N2   49.077.555.580
   25SOL N1   50   -.020   -.095.359
   25SOL N2   51.034   -.124.439
   26SOL N1   52.027   -.266.117
   26SOL N2   53.008   -.362.138
   27SOL N1   54   -.173.922.612
   27SOL N2   55   -.078.893.620
   28SOL N1   56   -.221   -.754.432
   28SOL N2   57   -.135   -.752.380
   29SOL N1   58.113.737   -.265
   29SOL N2   59.201.724   -.220
   30SOL N1   60.613   -.497.726
   30SOL N2   61.564   -.584.735
   31SOL N1   62   -.569   -.634   -.439
   31SOL N2   63   -.532   -.707   -.497
   32SOL N1   64.809.004.502
   32SOL N2   65.849.095.493
   33SOL N1   66.197   -.886   -.598
   33SOL N2   67.286   -.931   -.612
   34SOL N1   69   -.337   -.863.190
   34SOL N2   90   -.400   -.939.203
   35SOL N1   91   -.675   -.070   -.246
   35SOL N2   92   -.651   -.010   -.322
   36SOL N1   93.317.251   -.061
   36SOL N2   94.388.322   -.055
   37SOL N1   95   -.396   -.445   -.909
   37SOL N2   96   -.455   -.439   -.829
   38SOL N1   97   -.195   -.148.572
   38SOL N2   98   -.236   -.171.484
   39SOL N1   99.598.729.270
   39SOL N2  100.622.798.202
   40SOL N1  101   -.581.345   -.918
   40SOL N2  102   -.667.295   -.931
   41SOL N1  103   -.286   -.200.307
   41SOL N2  104   -.197   -.154.310
   42SOL N1  105.807.605   -.397
   42SOL N2  106.760.602   -.308
   43SOL N1  107   -.468.469   -.188
   43SOL N2  108   -.488.512   -.100
   44SOL N1  109   -.889.890   -.290
   44SOL N2  110   -.843.806   -.319
   45SOL N1  111   -.871.410   -.620
   45SOL N2  112   -.948.444   -.566
   46SOL N1  113   -.821.701.429
   46SOL N2  114   -.795.697.525
   47SOL N1  115.076.811.789
   47SOL N2  116.175.799.798
   48SOL N1  117.130   -.041   -.291
   48SOL N2  118.120   -.056   -.192
   49SOL N1  118.865.348.195
   49SOL N2  120.924.411.146
   50SOL N1  121   -.143.585   -.031
   50SOL N2  122   -.169.674   -.067
   51SOL N1  123   -.500   -.718.545
   51SOL N2  124   -.417   -.747.497
   52SOL N1  

Re: [gmx-users] invalid line

[Justin A. Lemkul]

sarah k wrote:

dear gromacs users,

I'm solvating my protein in nitrogen box. I have changed my
spc216.gro, spc.itp and spce.itp files. I face the following error.


Changed?  In what way?  If you're solvating with nitrogen, why are you dealing 
with water coordinates and topologies?



How can I fix it?

invalid line in /usr/share/gromacs/top/spc216.gro for atom 407:
  0.41200  0.41200  0.41200



In spc216.gro, there are 648 atoms.  If you've somehow manipulated that file 
such that it contains fewer atoms (or something else entirely), whatever Gromacs 
tool you're using will anticipate 648 atoms.  It seems that instead of atom 407, 
it's finding the box vectors.


-Justin


thanks in advance.

Best regards,
Fatemeh Keshavarz



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] OPLS parametrizaton

[Marcelo Silva]

Em 02-04-2011 0:33, Justin A. Lemkul escreveu:



Marcelo Silva wrote:

Hi,

I am trying to simulate mixtures of ethanol and trifluoroethanol and 
I would like to use the same parameters used on OPLS parametrization.


On the OPLS1996 paper the authors starts by stating that they've used 
267 molecules and "The box size varied from approximately 26 26  26 
Å for methanol to 37  37  37 Å for cyclohexane". In my simulations 
I am considering using 500 molecules (each box vector would be around 
37 Å).


"In most cases, the intermolecular nonbonded interactions were 
truncated at 11Å based on roughly the center-of-mass separations with 
quadratic smoothing of the interaction energy to zero over the last 
0.5 Å (...) A standard correction was made for the Lennard-Jones 
interactions neglected beyond the cutoff."


Trying to interpret what is written I think the correct way to treat 
cut-offs and energy corrections would be like this:


---
Cut-offs

rlist= 1.4
coulombtype  = Reaction-field-zero
rcoulomb = 1.1
rcuolomb_shift  = 0.6
vdwtype   = shift
rvdw = 1.1
rvdw_switch= 0.6

Dispersion Correction

DispCorr = EnerPress

---

However I have some doubts because I'm using a box with a different 
number of molecules/ different size (should I change the cutoffs to 
15Å like it was for cyclohexane?) and I'm not sure about using 
Reaction-field-zero instead of the shift function for coulombic 
interactions.


Could you please help me confirm this parameters so I can run a 
simulation in the same conditions as OPLS was parameterized (although 
using MC and not MD).




I don't think there is a perfectly clear answer to this.  OPLS was 
initially designed for MC with some special functional forms and is 
now applied to MD using all manner of settings.  Commonly, one sees 
rcoulomb=rvdw=rlist=1.0 or 1.4 in conjunction with PME.  There have 
been a variety of systematic force field comparisons in recent years.  
You should consult those to see what their specific recommendations 
are with respect to proper settings, although many of them focus on 
proteins.


-Justin


Best regards,

Marcelo




Just to test it, I used this options (nstlist = 5 with timestep 1fs):

; Cut-offs

rlist= 1.4
coulombtype  = Switch
rcoulomb = 1.1
rcuolomb_shift  = 1.05
vdwtype   = Switch
rvdw = 1.1
rvdw_switch= 1.05

; Dispersion Correction

DispCorr = EnerPres

and compared to vdw plain cutoff at 1.1 and PME with cutoff 1.1 nm 
(rlist = 1.1 nm also). The big difference in the output seems to be with 
the Coulomb (SR) term:


-1.25490e+05 kj/mol with Switch
-5.38895e+03  kj/mol   with PME

With switch I get a low density for ethanol (about 0.3 g/ml). What could 
be the problem with the simulation using switch? By the way does gromacs 
use a different switch function depending on the forcefield?


Best regards,

Marcelo
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Re: [gmx-users] OPLS parametrizaton

[Justin A. Lemkul]

Marcelo Silva wrote:

Em 02-04-2011 0:33, Justin A. Lemkul escreveu:



Marcelo Silva wrote:

Hi,

I am trying to simulate mixtures of ethanol and trifluoroethanol and 
I would like to use the same parameters used on OPLS parametrization.


On the OPLS1996 paper the authors starts by stating that they've used 
267 molecules and "The box size varied from approximately 26 26  26 
Å for methanol to 37  37  37 Å for cyclohexane". In my simulations 
I am considering using 500 molecules (each box vector would be around 
37 Å).


"In most cases, the intermolecular nonbonded interactions were 
truncated at 11Å based on roughly the center-of-mass separations with 
quadratic smoothing of the interaction energy to zero over the last 
0.5 Å (...) A standard correction was made for the Lennard-Jones 
interactions neglected beyond the cutoff."


Trying to interpret what is written I think the correct way to treat 
cut-offs and energy corrections would be like this:


---
Cut-offs

rlist= 1.4
coulombtype  = Reaction-field-zero
rcoulomb = 1.1
rcuolomb_shift  = 0.6
vdwtype   = shift
rvdw = 1.1
rvdw_switch= 0.6

Dispersion Correction

DispCorr = EnerPress

---

However I have some doubts because I'm using a box with a different 
number of molecules/ different size (should I change the cutoffs to 
15Å like it was for cyclohexane?) and I'm not sure about using 
Reaction-field-zero instead of the shift function for coulombic 
interactions.


Could you please help me confirm this parameters so I can run a 
simulation in the same conditions as OPLS was parameterized (although 
using MC and not MD).




I don't think there is a perfectly clear answer to this.  OPLS was 
initially designed for MC with some special functional forms and is 
now applied to MD using all manner of settings.  Commonly, one sees 
rcoulomb=rvdw=rlist=1.0 or 1.4 in conjunction with PME.  There have 
been a variety of systematic force field comparisons in recent years.  
You should consult those to see what their specific recommendations 
are with respect to proper settings, although many of them focus on 
proteins.


-Justin


Best regards,

Marcelo




Just to test it, I used this options (nstlist = 5 with timestep 1fs):

; Cut-offs

rlist= 1.4
coulombtype  = Switch
rcoulomb = 1.1
rcuolomb_shift  = 1.05
vdwtype   = Switch
rvdw = 1.1
rvdw_switch= 1.05

; Dispersion Correction

DispCorr = EnerPres

and compared to vdw plain cutoff at 1.1 and PME with cutoff 1.1 nm 
(rlist = 1.1 nm also). The big difference in the output seems to be with 
the Coulomb (SR) term:


-1.25490e+05 kj/mol with Switch
-5.38895e+03  kj/mol   with PME

With switch I get a low density for ethanol (about 0.3 g/ml). What could 
be the problem with the simulation using switch? By the way does gromacs 
use a different switch function depending on the forcefield?




The manual warns of artifacts that arise from switching functions.  So there is 
not a "problem" with switch, per se, rather an intrinsic limitation in accuracy. 
 I would imagine the low density arises from completely neglecting (via 
truncation) any long-range electrostatics terms that PME (and to some extent, 
other long-range methods) otherwise includes.


The switch function is not force field-dependent.

-Justin


Best regards,

Marcelo



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] invalid line

[Mark Abraham]

On 6/04/2011 4:30 AM, sarah k wrote:

dear gromacs users,

I'm solvating my protein in nitrogen box. I have changed my
spc216.gro, spc.itp and spce.itp files.


Don't. In the last 48 hours, I posted a procedure that used genconf to 
make a box of solvent of a given density.



  I face the following error.
How can I fix it?

invalid line in /usr/share/gromacs/top/spc216.gro for atom 407:


Definitely do not modify your installed GROMACS files. Copy things to 
your working directory and change them there. Otherwise, some poor 
person later who uses spc216.gro will have some inexplicable problem and 
post here and nobody will have any idea what could be wrong. genbox lets 
you use any file of solvent you specify - see genbox -h.


Use spc.itp as a model for the .itp file, but again, copy the file, 
rename it and then change the contents.


Mark


   0.41200  0.41200  0.41200

thanks in advance.

Best regards,
Fatemeh Keshavarz


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[gmx-users] FEP and loss of performance

[chris . neale]

I don't know if it is possible or not. I think that you can enhance  
your chances of developer attention if you develop a small and simple  
test system that reproduces the slowdown and very explicitly state  
your case for why you can't use some other method. I would suggest  
posting that to the mailing list and, if you don't get any response,  
post it as an enhancement request on the redmine page (or whatever has  
taken over from bugzilla).


Good luck,
Chris.

-- original message --


Yes i am testing the possibility to perform an Hamiltonian-REMD
Energy barriers can be overcome  increasing the temperature system or scaling
potential energy  with a lambda value, these methods are "equivalent".
Both have advantages and disavantages, at this stage it is not the right place
to debate on it. The main problem seems to be how to overcome to the the loss
of gromacs performance in such calculation.  At this moment it seems an
intrinsic code problem.
Is it possible?


 >> Dear Chris and Justin
>>
>>/  Thank you for your precious suggestions

/>>/  This is a test that i perform in a single machine with 8 cores
/>>/  and gromacs 4.5.4.
/>>/
/>>/  I am trying  to enhance the  sampling of a protein using the
decoupling scheme />>/  of the free energy module of gromacs.  However when
i decouple only the />>/  protein, the protein collapsed. Because i
simulated in NVT i thought that />>/  this was an effect of the solvent. I
was trying to decouple also the solvent />>/  to understand the system
behavior.
/>>/
/>

>Rather than suspect that the solvent is the problem, it's more likely that
>decoupling an entire protein simply isn't stable.  I have never tried
> anything that enormous, but the volume change in the system could be
> unstable, along with any number of factors, depending on how you approach
> it.
>
>If you're looking for better sampling, REMD is a much more robust approach
> than trying to manipulate the interactions of huge parts of your system
> using the free energy code.

Presumably Luca is interested in some type of hamiltonian exchange where
lambda represents the interactions between the protein and the solvent?
This can actually be a useful method for enhancing sampling. I think it's
dangerous if we rely to heavily on "try something else". I still see no
methodological reason a priori why there should be any actual slowdown, so
that makes me think that it's an implementation thing, and there is at
least the possibility that this is something that could be fixed as an
enhancement.

Chris.


-Justin

>/   I expected a loss of performance, but not so drastic.

/>/  Luca
/>/
/>>/  Load balancing problems I can understand, but why would it take
longer />>/  in absolute time? I would have thought that some nodes would
simple be />>/  sitting idle, but this should not cause an increase in the
overall />>/  simulation time (15x at that!).
/>>/
/>>/  There must be some extra communication?
/>>/
/>>/  I agree with Justin that this seems like a strange thing to do, but
/>>/  still I think that there must be some underlying coding issue
(probably />>/  one that only exists because of a reasonable assumption
that nobody />>/  would annihilate the largest part of their system).
/>>/
/>>/  Chris.
/>>/
/>>/  Luca Bellucci wrote:
/>>>/  /  Hi Chris,
/>>/  />/  thank for the suggestions,
/>>/  />/  in the previous mail there is a mistake because
/>>/  />/  couple-moltype = SOL (for solvent) and not "Protein_chaim_P".
/>>/  />/  Now the problem of the load balance seems reasonable, because
/>>/  />/  the water box is large ~9.0 nm.
/>>/  /
/>>/  Now your outcome makes a lot more sense.  You're decoupling all of
the />>/  solvent? I don't see how that is going to be physically stable or
terribly /


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Re: [gmx-users] How to merge 2 top-files

[Peter C. Lai]

In this case,
Can't you just use pdb2gmx to regenerate the topology file from the merged
gro which will resolve the separate moleculechains for you?

On 2011-03-30 04:25:34AM -0500, Mark Abraham wrote:
> On 30/03/2011 8:14 PM, Ghassen Hassani wrote:
> 
> Dear Friends,
> Right now i am working on the docking of a small ligand to a receptor. in 
> order to begin md simulations in gromacs, i need to create some files..
> 
> I have already docked my ligand to the receptor and i have those files:
>- ligand_receptor.gro
>- posre.itp (for only the receptor !!)
> 
> 
> I have 2 Questions:
> 
> 1- How can i expand the posre.itp file to also include the ligand.data ?
> 
> 
> Don't. The position restraints file is intended to be #included from within a 
> [moleculetype]. You have two, so you need two position restraint files, each 
> #included from a different, appropriate place. The GROMACS tool genrestr can 
> help generate that for the ligand.
> 
> that means how can i do to create a posre.itp-file for my 
> ligand_receptor-komplex ?
> 
> 
> Don't.
> 
> 
> 2- I have 2 separate top-files: ligand.top (from the prodrg-server) and the 
> receptor.top file. How can i "merge" the 2 files and obtain the file 
> ligand_receptor.top for the whole ligand-receptor-komplex ?
> 
> 
> You need to convert one of your [moleculetype] definitions in one of your 
> .top files into an .itp file 
> (http://www.gromacs.org/Documentation/File_Formats/.itp_File) and #include it 
> suitably from the other. See chapter 5 of the manual for details. This is 
> tricky, do your homework first. Note that you should take note of the warning 
> here: http://www.gromacs.org/Downloads/Related_Software/PRODRG
> 
> 
> 
> 
> 
> 
> Many thanx, please email-me on my adress: 
> greendreams1...@yahoo.de
> 
> Yours.
> 
> 
> 
> 
> 
> No, that is against accepted netiquette. If your question is worth answering, 
> then that answer is worth broadcasting and archiving so others can learn from 
> it.
> 
> Mark

> -- 
> gmx-users mailing listgmx-users@gromacs.org
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] How to merge 2 top-files

[Justin A. Lemkul]

Peter C. Lai wrote:

In this case,
Can't you just use pdb2gmx to regenerate the topology file from the merged
gro which will resolve the separate moleculechains for you?



Only if you really feel like re-writing the ligand topology from scratch as an 
.rtp entry to be processed by pdb2gmx, and then attempt to make a merged 
moleculetype.  In short, yes, it's possible to treat a protein-ligand complex as 
a single entity, but it's probably not worth the effort when it is far simpler 
to #include a ligand topology and #include a position restraint file for it. 
This approach also provides considerably more flexibility in terms of 
restraining the protein and ligand independently, which may be required for 
various applications.


-Justin


On 2011-03-30 04:25:34AM -0500, Mark Abraham wrote:

On 30/03/2011 8:14 PM, Ghassen Hassani wrote:

Dear Friends,
Right now i am working on the docking of a small ligand to a receptor. in order 
to begin md simulations in gromacs, i need to create some files..

I have already docked my ligand to the receptor and i have those files:
   - ligand_receptor.gro
   - posre.itp (for only the receptor !!)


I have 2 Questions:

1- How can i expand the posre.itp file to also include the ligand.data ?


Don't. The position restraints file is intended to be #included from within a 
[moleculetype]. You have two, so you need two position restraint files, each 
#included from a different, appropriate place. The GROMACS tool genrestr can 
help generate that for the ligand.

that means how can i do to create a posre.itp-file for my 
ligand_receptor-komplex ?


Don't.


2- I have 2 separate top-files: ligand.top (from the prodrg-server) and the receptor.top 
file. How can i "merge" the 2 files and obtain the file ligand_receptor.top for 
the whole ligand-receptor-komplex ?


You need to convert one of your [moleculetype] definitions in one of your .top 
files into an .itp file 
(http://www.gromacs.org/Documentation/File_Formats/.itp_File) and #include it 
suitably from the other. See chapter 5 of the manual for details. This is 
tricky, do your homework first. Note that you should take note of the warning 
here: http://www.gromacs.org/Downloads/Related_Software/PRODRG






Many thanx, please email-me on my adress: 
greendreams1...@yahoo.de

Yours.





No, that is against accepted netiquette. If your question is worth answering, 
then that answer is worth broadcasting and archiving so others can learn from 
it.

Mark



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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] How to remove charge of 5e-2 ??

[김현식]

> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
> 
> On 5/04/2011 11:17 PM, Hyunsik wrote:
> > Dear experts,
> >
> > Hi,
> >
> > When prepare a system, the system had +5.5. So I add 5 CL- ion to 
> > neutralize.
> >
> > But as you know, the Cl charge is -1 and there still is 5e-2. how can i 
> > remove that.
> 
> Your statements are inconsistent. If you had 5.5 charge and added five 
> chloride ions, you could not end up with 0.05.

  oh.. I have mistaken.. I had 5.005 of the system charge. 
  
  So even if added five choride ions, the system charge is not zero. there was 
0.005 

  that is partial charge??  If like that, topology is broken or something 
wrong? abnormal??
  
  Thank you,

  Hyun

> 
> Mark
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] How to remove charge of 5e-2 ??

[Justin A. Lemkul]

김현식 wrote:



 > Date: Tue, 5 Apr 2011 23:43:19 +1000
 > From: mark.abra...@anu.edu.au
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
 >
 > On 5/04/2011 11:17 PM, Hyunsik wrote:
 > > Dear experts,
 > >
 > > Hi,
 > >
 > > When prepare a system, the system had +5.5. So I add 5 CL- ion to 
neutralize.

 > >
 > > But as you know, the Cl charge is -1 and there still is 5e-2. how 
can i remove that.

 >
 > Your statements are inconsistent. If you had 5.5 charge and added five
 > chloride ions, you could not end up with 0.05.

  oh.. I have mistaken.. I had 5.005 of the system charge.
 
  So even if added five choride ions, the system charge is not zero. 
there was 0.005


  that is partial charge??  If like that, topology is broken or 
something wrong? abnormal??
 


Maybe, maybe not.  Rounding errors could account for this difference, especially 
if your system is very large.  Still, you should inspect your 
topology/topologies for inconsistencies.  If pdb2gmx created the topology, keep 
an eye on the "qtot" column for a running total of the charge.  If you've made 
or adjusted any topologies on your own, double-check your work.  If everything 
looks correct, then the difference is likely a consequence of floating-point 
math and nothing more.


-Justin


  Thank you,

  Hyun

 >
 > Mark
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] are TPR files compatible across minor version changes?

[Peter C. Lai]

Are TPR files compatible across minor gromacs version changes?
Like if I have a TPR generated under 4.5.3 can I feed it into mdrun on 4.5.4
or should I re-grompp my initial files?

Thanks
-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] are TPR files compatible across minor version changes?

[Justin A. Lemkul]

Peter C. Lai wrote:

Are TPR files compatible across minor gromacs version changes?
Like if I have a TPR generated under 4.5.3 can I feed it into mdrun on 4.5.4
or should I re-grompp my initial files?



Minor versions shouldn't present a problem.  According to src/gmxlib/tpxio.c, 
the .tpr version hasn't incremented between 4.5.3 and 4.5.4 and generally, 
Gromacs programs are backwards-compatible.  But since it just takes a few 
seconds to run grompp to be sure, I don't see why you wouldn't.


-Justin


Thanks


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy

[zhongjin]

Hi to all,
I want to know what do Coul-SR,LJ-SR,Coul-14 and LJ-14 mean in g_energy ? I 
do know SR stands for short range.But do short range really mean? Thanks!
Coul-SR:K-SOL   46  LJ-SR:K-SOL 47  Coul-14:K-SOL   48  LJ-14:K-SOL
   Zhongjin He-- 
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Re: [gmx-users] what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy

[Justin A. Lemkul]

zhongjin wrote:

Hi to all,
I want to know what do Coul-SR,LJ-SR,Coul-14 and LJ-14 mean in g_energy 
? I do know SR stands for short range.But do short range really mean? 


http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy

-Justin


Thanks!
Coul-SR:K-SOL 46 LJ-SR:K-SOL 47 Coul-14:K-SOL 48 LJ-14:K-SOL
Zhongjin He



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] help on converting charmm/cgenff parameters to gromacs

[Peter C. Lai]

Hello

I am constructing a ligand for which I wish to use the new Charmm CGenFF 
parameters (a long aliphatic ketone).

I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:

For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331 
in CGenFF; they are both to represent alkane CH3 carbons. Same with
CTL2 -> CG321. In my case I am particularly interested in CGenFF's 
parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3 
(without any associated carboxylic bias or bias from non-carbons found
in other parameters. For example C=O in amino acid backbone appears in
ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of 
5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be 
different and especially the nonbonded interactions since we've replaced
N with C and we have an extra H etc. etc.).

My ligand for now is pretty simple:

  OG2D3
   ||
CG331-CG321-...-CG321-CG2O5-CG331

or, in c36 lipid/prot terms:
   O  
   ||
CTL3-CTL2-...-CTL2-C-C-CTL3

How would I convert the relevant atoms in CGenFF's prm file to both 
dihedral and nonbonded interaction .itp for gromacs? I tried using Mark's 
perl scripts and it is giving me wrong LJ terms as well as not picking up 
any 1,4 interactions (not to mention it has no knowledge of Par's 
functype 9 for converting Charmm dihderals - we should no longer be using
R-B functions).

Finally, a slightly (un)related question:
in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we
usually give it -0.18 for associated molecules in the rtp? Is there 
something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files
which makes sense to me).

-- 
===
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst   | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
p...@uab.edu  | Birmingham AL 35294-4461
(205) 690-0808   |
===

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Re: [gmx-users] How to remove charge of 5e-2 ??

[mohsen ramezanpour]

Dear Dr.Justin

I had the same problem.
I modified the charges and charge groupsin the  topology of a drug.the net
charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:

NOTE:The system has non-zero total charge: 3.03e00
I continued simulation and ignored it!
Because:
1- I checked my protein.top and qtot was 3
2-the net charge of my drug was 0
3-Besides,all charges have 3 digit precision,How can it have 0.03
additional charge?!

What is your point of view?
Thanks in advance for your reply


On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul  wrote:

>
>
> 김현식 wrote:
>
>>
>>
>>  > Date: Tue, 5 Apr 2011 23:43:19 +1000
>>  > From: mark.abra...@anu.edu.au
>>  > To: gmx-users@gromacs.org
>>  > Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>>  >
>>  > On 5/04/2011 11:17 PM, Hyunsik wrote:
>>  > > Dear experts,
>>  > >
>>  > > Hi,
>>  > >
>>  > > When prepare a system, the system had +5.5. So I add 5 CL- ion to
>> neutralize.
>>  > >
>>  > > But as you know, the Cl charge is -1 and there still is 5e-2. how can
>> i remove that.
>>  >
>>  > Your statements are inconsistent. If you had 5.5 charge and added five
>>  > chloride ions, you could not end up with 0.05.
>>
>>  oh.. I have mistaken.. I had 5.005 of the system charge.
>>   So even if added five choride ions, the system charge is not zero. there
>> was 0.005
>>
>>  that is partial charge??  If like that, topology is broken or something
>> wrong? abnormal??
>>
>>
>
> Maybe, maybe not.  Rounding errors could account for this difference,
> especially if your system is very large.  Still, you should inspect your
> topology/topologies for inconsistencies.  If pdb2gmx created the topology,
> keep an eye on the "qtot" column for a running total of the charge.  If
> you've made or adjusted any topologies on your own, double-check your work.
>  If everything looks correct, then the difference is likely a consequence of
> floating-point math and nothing more.
>
> -Justin
>
>
>   Thank you,
>>
>>  Hyun
>>
>>  >
>>  > Mark
>>  > --
>>  > gmx-users mailing list gmx-users@gromacs.org
>>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>  > Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>  > Please don't post (un)subscribe requests to the list. Use the
>>  > www interface or send it to gmx-users-requ...@gromacs.org.
>>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
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Re: [gmx-users] How to remove charge of 5e-2 ??

[mohsen ramezanpour]

Dear Dr.Justin

What can we do (how can neutralize system) if the total charge of our system
was not integer?
I think  there is not any solution and we have to simulate a charged system
not a neutral.
Am I right?
Thanks in advance

On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear Dr.Justin
>
> I had the same problem.
> I modified the charges and charge groupsin the  topology of a drug.the net
> charge of it is zero(I am sure)
> though,when I used pdb2gmx it resulted a NOTE like the following:
>
> NOTE:The system has non-zero total charge: 3.03e00
> I continued simulation and ignored it!
> Because:
> 1- I checked my protein.top and qtot was 3
> 2-the net charge of my drug was 0
> 3-Besides,all charges have 3 digit precision,How can it have 0.03
> additional charge?!
>
> What is your point of view?
> Thanks in advance for your reply
>
>
>
> On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul  wrote:
>
>>
>>
>> 김현식 wrote:
>>
>>>
>>>
>>>  > Date: Tue, 5 Apr 2011 23:43:19 +1000
>>>  > From: mark.abra...@anu.edu.au
>>>  > To: gmx-users@gromacs.org
>>>  > Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>>>  >
>>>  > On 5/04/2011 11:17 PM, Hyunsik wrote:
>>>  > > Dear experts,
>>>  > >
>>>  > > Hi,
>>>  > >
>>>  > > When prepare a system, the system had +5.5. So I add 5 CL- ion to
>>> neutralize.
>>>  > >
>>>  > > But as you know, the Cl charge is -1 and there still is 5e-2. how
>>> can i remove that.
>>>  >
>>>  > Your statements are inconsistent. If you had 5.5 charge and added five
>>>  > chloride ions, you could not end up with 0.05.
>>>
>>>  oh.. I have mistaken.. I had 5.005 of the system charge.
>>>   So even if added five choride ions, the system charge is not zero.
>>> there was 0.005
>>>
>>>  that is partial charge??  If like that, topology is broken or something
>>> wrong? abnormal??
>>>
>>>
>>
>> Maybe, maybe not.  Rounding errors could account for this difference,
>> especially if your system is very large.  Still, you should inspect your
>> topology/topologies for inconsistencies.  If pdb2gmx created the topology,
>> keep an eye on the "qtot" column for a running total of the charge.  If
>> you've made or adjusted any topologies on your own, double-check your work.
>>  If everything looks correct, then the difference is likely a consequence of
>> floating-point math and nothing more.
>>
>> -Justin
>>
>>
>>   Thank you,
>>>
>>>  Hyun
>>>
>>>  >
>>>  > Mark
>>>  > --
>>>  > gmx-users mailing list gmx-users@gromacs.org
>>>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>  > Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>  > Please don't post (un)subscribe requests to the list. Use the
>>>  > www interface or send it to gmx-users-requ...@gromacs.org.
>>>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

[Mark Abraham]

On 6/04/2011 2:51 PM, Peter C. Lai wrote:

Hello

I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).

I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:

For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331
in CGenFF; they are both to represent alkane CH3 carbons. Same with
CTL2 ->  CG321. In my case I am particularly interested in CGenFF's
parameterization of a ketone carbonyl and oxygen: CG2O5 and OG2D3
(without any associated carboxylic bias or bias from non-carbons found
in other parameters. For example C=O in amino acid backbone appears in
ffbonded.itp as 5.188e+05 for kB whereas Mark's script yielded a kB of
5.858e+05 for CG2O5=OG2D3, not to mention the bond angles should be
different and especially the nonbonded interactions since we've replaced
N with C and we have an extra H etc. etc.).

My ligand for now is pretty simple:

   OG2D3
||
CG331-CG321-...-CG321-CG2O5-CG331

or, in c36 lipid/prot terms:
O
||
CTL3-CTL2-...-CTL2-C-C-CTL3

How would I convert the relevant atoms in CGenFF's prm file to both
dihedral and nonbonded interaction .itp for gromacs?


The standard CHARMM .prm files give an indication of how the parameters 
will be used, so it's just a matter of converting units and taking care 
of any constants.



  I tried using Mark's
perl scripts and it is giving me wrong LJ terms as well as not picking up
any 1,4 interactions (not to mention it has no knowledge of Par's
functype 9 for converting Charmm dihderals - we should no longer be using
R-B functions).


This script predates dihedral functype 9, and implements a 
post-processing approach to deal with LJ, 1-4 and some dihedrals. I 
assume you haven't done the latter. In any case, the form of my 
solutions do not mesh at all with Par's solutions - forget about my scripts.


You seem to be only interested in about two atom types, so I'd expect 
you can convert all the relevant things by hand in under an hour.



Finally, a slightly (un)related question:
in ffnonbonded.itp, why does CTL2 get a charge of 0.05 when in reality we
usually give it -0.18 for associated molecules in the rtp? Is there
something I'm missing there? (CTL3 has -0.27 in both the itp and rtp files
which makes sense to me).


Sounds like a glitch when the file was written - I guess some other 
carbon also has 0.05 and this was copied and pasted. In any case, the 
charges in ffnonbonded.itp are never used by pdb2gmx, because 
precedence-taking residue-specific charges are defined in the .rtp. If 
one were to use some other tool for generating topologies, I don't know 
whether charges missing from a [moleculetype] definition are looked up 
in ffnonbonded.itp.


Mark
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Re: [gmx-users] How to remove charge of 5e-2 ??

[Mark Abraham]

On 6/04/2011 4:42 PM, mohsen ramezanpour wrote:

Dear Dr.Justin

I had the same problem.
I modified the charges and charge groupsin the  topology of a drug.the 
net charge of it is zero(I am sure)

though,when I used pdb2gmx it resulted a NOTE like the following:

NOTE:The system has non-zero total charge: 3.03e00
I continued simulation and ignored it!
Because:
1- I checked my protein.top and qtot was 3
2-the net charge of my drug was 0
3-Besides,all charges have 3 digit precision,How can it have 0.03 
additional charge?!


See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

Mark



What is your point of view?
Thanks in advance for your reply


On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul > wrote:




김현식 wrote:



> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au 
> To: gmx-users@gromacs.org 
> Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>
> On 5/04/2011 11:17 PM, Hyunsik wrote:
> > Dear experts,
> >
> > Hi,
> >
> > When prepare a system, the system had +5.5. So I add 5 CL-
ion to neutralize.
> >
> > But as you know, the Cl charge is -1 and there still is
5e-2. how can i remove that.
>
> Your statements are inconsistent. If you had 5.5 charge and
added five
> chloride ions, you could not end up with 0.05.

 oh.. I have mistaken.. I had 5.005 of the system charge.
  So even if added five choride ions, the system charge is not
zero. there was 0.005

 that is partial charge??  If like that, topology is broken or
something wrong? abnormal??


Maybe, maybe not.  Rounding errors could account for this
difference, especially if your system is very large.  Still, you
should inspect your topology/topologies for inconsistencies.  If
pdb2gmx created the topology, keep an eye on the "qtot" column for
a running total of the charge.  If you've made or adjusted any
topologies on your own, double-check your work.  If everything
looks correct, then the difference is likely a consequence of
floating-point math and nothing more.

-Justin


 Thank you,

 Hyun

>
> Mark
> --
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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] How to remove charge of 5e-2 ??

[Mark Abraham]

On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:

Dear Dr.Justin

What can we do (how can neutralize system) if the total charge of our 
system was not integer?
I think  there is not any solution and we have to simulate a charged 
system not a neutral.

Am I right?


I suspect every tutorial for simulating proteins in water deals with the 
need for counter-ions, and the technique for generating them.


Mark


Thanks in advance

On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour 
mailto:ramezanpour.moh...@gmail.com>> 
wrote:


Dear Dr.Justin

I had the same problem.
I modified the charges and charge groupsin the  topology of a
drug.the net charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:

NOTE:The system has non-zero total charge: 3.03e00
I continued simulation and ignored it!
Because:
1- I checked my protein.top and qtot was 3
2-the net charge of my drug was 0
3-Besides,all charges have 3 digit precision,How can it have
0.03 additional charge?!

What is your point of view?
Thanks in advance for your reply



On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



김현식 wrote:



> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au

> To: gmx-users@gromacs.org 
> Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>
> On 5/04/2011 11:17 PM, Hyunsik wrote:
> > Dear experts,
> >
> > Hi,
> >
> > When prepare a system, the system had +5.5. So I add 5
CL- ion to neutralize.
> >
> > But as you know, the Cl charge is -1 and there still
is 5e-2. how can i remove that.
>
> Your statements are inconsistent. If you had 5.5 charge
and added five
> chloride ions, you could not end up with 0.05.

 oh.. I have mistaken.. I had 5.005 of the system charge.
  So even if added five choride ions, the system charge is
not zero. there was 0.005

 that is partial charge??  If like that, topology is
broken or something wrong? abnormal??


Maybe, maybe not.  Rounding errors could account for this
difference, especially if your system is very large.  Still,
you should inspect your topology/topologies for
inconsistencies.  If pdb2gmx created the topology, keep an eye
on the "qtot" column for a running total of the charge.  If
you've made or adjusted any topologies on your own,
double-check your work.  If everything looks correct, then the
difference is likely a consequence of floating-point math and
nothing more.

-Justin


 Thank you,

 Hyun

>
> Mark
> --
> gmx-users mailing list gmx-users@gromacs.org

> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
> Please don't post (un)subscribe requests to the list.
Use the
> www interface or send it to
gmx-users-requ...@gromacs.org
.
> Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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